A combined steepest descent and genetic algorithm (SD/GA) approach for the optimization of solvation parameters

Abstract

An accurate solvation model is essential for computer modeling of protein folding and other biomolecular self-assembly processes. Compared to explicit solvent models, implicit solvent models, such as the Poisson-Boltzmann (PB) with solvent accessible surface area model (PB/SA), offer a much faster speed—the most compelling reason for the popularity of these implicit solvent models. Since these implicit solvent models typically use empirical parameters, such as atomic radii and the surface tensions, an optimal fit of these parameters is crucial for the final accuracy of properties such as solvation free energy and folding free energy. In this paper, we proposed a combined approach, namely SD/GA, which takes the advantage of both local optimization with the steepest descent (SD), and global optimization with the genetic algorithm (GA), for parameters optimization in multi-dimensional space. The SD/GA method is then applied to the optimization of solvation parameters in the non-polar cavity term of the PB/SA model. The results show that the newly optimized parameters from SD/GA not only increase the accuracy in the solvation free energies for ∼200 organic molecules, but also significantly improve the free energy landscape of a β-hairpin folding. The current SD/GA method can be readily applied to other multi-dimensional parameter space optimization as well.

Keywords:

• Parameter optimization
• Genetic algorithm
• Solvation parameters
• Poisson-Boltzmann
• Steepest descent

Acknowledgements

We would like to thank Barry Honig for sending us the Delphi code for the Poisson-Boltzmann continuum solvent model in a previous study, and Ray Luo, Emilio Gallicchio and Ron Levy for many helpful discussions.